0.1 Approach

Models are at the core of modern phylogenetic biology. Models are usually taught in the context of phylogenetic inference, where they are used to look backward in time. This seems to me a bit like teaching students to master driving in reverse before you show them how to drive forward down a road. Phylogenetic models are generative - they explain how data are created under specific evolutionary processes. They are therefore more intuitive to understand in the context of generating data, proceeding in time from ancestral states forward to future states. I therefore focus first on building an intuitive understanding of models in the context of simulation, and only after that apply models to inference and other tasks that look back in time.

0.2 Using this book

This book is intended both for the self directed learner, and for use in a course.

I wrote it as a text for my course, Phylogenetic Biology (Yale EEB354). We read one chapter a week. We review and discuss the reading on Tuesdays, and then on Thursdays do hands-on work, read papers from the literature, or share student projects.

0.3 Distribution

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. It is available to read online for free at, ensuring access to all students worldwide. If there is interest, I will also make paperbacks available for purchase at a reasonable price. Commercial use by others (e.g. the sale of printed copies by anyone other than the author) are not allowed.

This book was rendered from source code, available at, with bookdown (Xie 2016). If you are curious about how any of the figures or analyses were done you can examine the source code there.

Please submit any errors you find, typos, or suggestions that you have for improving the manuscript to the issue tracker at

0.4 Other resources

The following sites have a wide variety of material that is relevant to the theory and and practice of phylogenetic biology.

  • An extensive list of tools, tutorials, and examples of phylogenetic tools in the programming language R maintained by Briam O’Meara:

  • The Workshop on Molecular Evolution at Woods Hole. This is an intensive summer course on phylogenetics, with an emphasis on building phylogenetic trees. Check out the faculty pages for lecture pdfs:

  • The Applied Phylogenetics Workshop in Bodega Bay. This is another summer course on phylogenetics, but with a bit more emphasis on using phylogenies to test evolutionary questions:

The following books are great resources for learning more about phylogenetic biology:

  • Baum, D. and Smith, S. (2012). Tree Thinking. An Introduction to Phylogenetic Biology. Roberts Publishers.

  • Paradis, E. (2011) Analysis of Phylogenetics and Evolution with R. Springer

  • Felsenstein, J. (2004) Inferring phylogenies. Sinauer Associates.

  • Swofford, D. L., Olsen, G. J., Waddell, P. J., & Hillis, D. M. (1996). Phylogenetic inference. In: Molecular Systematics, Second Edition. eds: D. M. Hillis, C Moritz, & B. K. Mable. Sinauer Associates

The following books provide general computational background for the topics covered here:

0.5 License

0.6 Acknowledgements

Thanks in particular to the students of Yale EEB354 in the falls of 2020 (the first course I taught fully online) and 2022. This book started as a collection of lecture notes for this course. The students provided invaluable motivation, feedback, and patience. Thanks in particular to Lauren Mellenthin, the graduate teaching fellow for the course in 2020, and Namrata Ahuja, the teaching fellow in 2022. Members of my lab provided very helpful feedback when I posted new chapters. Steve Haddock and Felipe Zapata also provided close reads of most chapters, often within hours of completing first drafts. Thanks to Richard Hammack, author of Book of Proof, for his helpful advice on self publishing to facilitate student access.


Xie, Yihui. 2016. Bookdown: Authoring Books and Technical Documents with R Markdown. Boca Raton, Florida: Chapman; Hall/CRC.